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43 results for “ddRAD”
Green turtle ddRAD raw sequencing data
<p>The occasional westward transport of warm water of the Agulhas Current, 'Agulhas leakage', around southern Africa has been suggested to facilitate tropical marine connectivity between the Atlantic and Indian oceans, but the 'Agulhas leakage' hypothesis doesn't explain the signatures of eastward gene flow observed in many tropical marine fauna. We investigated an alternative hypothesis: the establishment of a warm-water corridor during comparatively warm interglacial periods. The 'warm-water corridor' hypothesis was investigated by studying the population genomic structure of Atlantic and Southwest Indian Ocean green turtles (<i>N </i><span>= 27) </span>using 12,035 genome-wide single nucleotide polymorphisms (SNPs) obtained via ddRAD sequencing. Model-based and multivariate clustering suggested a hierarchical population structure with two main Atlantic and Southwest Indian Ocean clusters, and a Caribbean and East Atlantic sub-cluster nested within the Atlantic cluster. Coalescent-based model selection supported a model where Southwest Indian Ocean and Caribbean populations diverged from the East Atlantic population during the transition from the last interglacial period (130 – 115 thousand years ago; kya) to the last glacial period (115 – 90 kya). The onset of the last glaciation appeared to isolate Atlantic and Southwest Indian Ocean green turtles into three refugia, which subsequently came into secondary contact in the Caribbean and Southwest Indian Ocean when global temperatures increased after the Last Glacial Maximum. Our findings support the establishment of a warm-water corridor facilitating tropical marine connectivity between the Atlantic and Southwest Indian Ocean during warm interglacials.</p>
Genome-wide SNP discovery in native American and Hungarian Robinia pseudoacacia genotypes using next-generation double-digest restriction-site-associated DNA sequencing (ddRAD-Seq)
<p>Initial filtered ddRADseq dataset with highly variable SNP markers from native American and Hungarian <em>Robinia pseudoacacia</em> L. individuals</p>
Key triggers of adaptive genetic variability of sessile oak [Q. petraea (Matt.) Liebl.] from the Balkan refugia: outlier detection and association of SNP loci from ddRAD-seq data
<p>Knowledge on the genetic composition of <em>Quercus petraea</em> in south-eastern Europe is limited despite the species' significant role in the re-colonisation of Europe during the Holocene, and the diverse climate and physical geography of the region. Therefore, it is imperative to conduct research on adaptation in sessile oak to better understand its ecological significance in the region. While large sets of SNPs have been developed for the species, there is a continued need for smaller sets of SNPs that are highly informative about the possible adaptation to this varied landscape. By using double digest restriction site associated DNA sequencing data from our previous study, we mapped RAD-tag sequences to the <em>Quercus robur</em> reference genome and identified a set of SNPs putatively related to drought stress-response. A total of 179 individuals from eighteen natural populations at sites covering heterogeneous climatic conditions in the southeastern natural distribution range of <em>Q. petraea</em> were genotyped. The detected highly polymorphic variant sites revealed three genetic clusters with a generally low level of genetic differentiation and balanced diversity among them but showed a north–southeast gradient. Selection tests showed nine outlier SNPs positioned in different functional regions. Genotype-environment association analysis of these markers yielded a total of 53 significant associations, explaining 2.4–16.6% of the total genetic variation. Our work exemplifies that adaptation to drought may be under natural selection in the examined <em>Q. petraea</em> populations.</p>
VCF files of ddRAD seq data of Bermuda petrel population
<p>Two VCF files resulted from two different filtering and analyses of ddRAD sequencing data of the endangered Bermuda petrel. The one_snp VCF contains only one snp per RAD locus, while the all_snps contained all SNPs in a RAD locus.</p>
ddRAD genotyping data
<p>This dataset includes raw sequences and metadata (barcodes) used for ddRAD genotyping in the publication:</p> <blockquote> <p>Stelzer, C.P., M. Pichler, P. Stadler, Genome streamlining and clonal erosion in nutrient-limited environments: a test using genome-size variable populations, <em>Evolution</em>, Volume 77, Issue 11, November 2023, Pages 2378–2391, <a href="https://doi.org/10.1093/evolut/qpad144">https://doi.org/10.1093/evolut/qpad144</a></p> </blockquote> <p>Please cite this study if you use the data.</p>
Green turtle ddRAD raw sequencing data
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A genomic data set of single‐nucleotide polymorphisms (SNPs) generated by ddRAD tag sequencing in Q. petraea (Matt.) Liebl. populations from Central-Eastern Europe and Balkan Peninsula
<p>This genomic dataset provides highly variable single-nucleotide polymorphism (SNP) markers from georeferenced natural <em>Quercus petraea</em> (Matt.) Liebl. populations collected in Bulgaria, Hungary, Romania, Serbia, Bosnia and Herzegovina, Kosovo and Albania. These SNP loci can be used to assess genetic diversity, differentiation, population structure, and can also be used to detect signatures of selection and local adaptation.</p>
Mergus octosetaceus ddRAD data (vcf file)
<p>This VCF file contains SNPs derived from 46 individuals of the <i>Mergus octosetaceus </i>species. The data was obtained using the Double digest restriction-site associated sequencing (ddRAD-seq) methodology and processed through the Stacks <i>de novo</i> pipeline.</p>
Divergence time estimation using ddRAD data and an isolation-with-migration model applied to water vole populations of Arvicola
<p>Molecular dating methods of population splits are crucial in evolutionary biology, but they present important difficulties due to the complexity of the genealogical relationships of genes and past migrations between populations. Using the double digest restriction-site associated DNA (ddRAD) technique and an isolation-with-migration (IM) model, we studied the evolutionary history of water vole populations of the genus <em>Arvicola</em>, a group of complex evolution with fossorial and semi-aquatic ecotypes. To do this, we first estimated mutation rates of ddRAD loci using a phylogenetic approach. An IM model was then used to estimate split times and other relevant demographic parameters. A set of 300 ddRAD loci that included 85 calibrated loci resulted in good mixing and model convergence. The results showed that the two populations of <em>A. scherman</em> present in the Iberian Peninsula split 34 thousand years ago, during the last glaciation. In addition, the much greater divergence from its sister species, <em>A. amphibius</em>, may help to clarify the controversial taxonomy of the genus. We conclude that this approach, based on ddRAD data and an IM model, is highly useful for analyzing the origin of populations and species.</p>
ddRAD data for: Multiple introductions and overwintering shape the progressive invasion of Aedes albopictus beyond the Alps
<p class="MsoNormal"><em><span>Aedes albopictus</span></em><span> originates from Southeast Asia and is considered one of the most invasive species globally. This mosquito </span><span>is a nuisance and a disease vector of significant public health relevance</span><span>. </span><span>In Europe, <em>Ae. albopictus</em> is firmly established and widespread south of the Alps, a mountain range that forms a formidable biogeographic barrier to many organisms. Recent reports of <em>Ae. albopictus</em> north of the Alps raise questions of 1) the origins of its recent invasion, and 2) if this mosquito has established overwintering populations north of the Alps. To answer these questions, </span><span>we analyzed population genomic data from >4000 genome-wide SNPs obtained through </span><span>double digest restriction-site associated DNA sequencing</span><span>. </span><span>We collected SNPs data from specimens from 6 sites in Switzerland, north and south of the Alps, and analyzed them together with specimens from other 33 European sites, 5 from the Americas, and 5 from its Asian native range. At a global level, we detected 4 genetic clusters with specimens from </span><span>Indonesia, Brazil and Japan as the most differentiated, whereas specimens from Europe, Hong Kong and USA largely overlapped</span><span>. Across the Alps, </span><span>we detected a weak genetic structure and high levels of genetic admixture, supporting a scenario of rapid and human-aided dispersal along transportation routes. While the genetic pattern suggests frequent re-introductions from Italian sources into Switzerland, t</span><span>he recovery of a pair of full siblings in two consecutive years in Strasbourg, France, suggests the presence of an overwintering population north of the Alps. </span><span>The finding of overwintering populations of <em>Ae. albopictus </em>north of the Alps and the expansion patterns points to an increased risk of further northwards expansion and the need for increased surveillance of mosquito populations in northern Europe.</span></p> <p> </p>
ddRAD sequencing of Fagus sylvatica sensu lato
<p>ddRAD sequencing data from Stacks (SNPs) along with corresponding information. Exon-only genotypes in file "genotypes_exons-only.7z".</p>
Illumina next generation ddRAD sequencing SNP data from: Contrasting genetic diversity and structure between endemic and widespread damselfishes are related to differing adaptive strategies
<p class="MsoNormal"><strong><u><span>Aim:</span></u></strong><span> Discerning when, where, and how processes of isolation lead to differing biogeography is especially complex for marine species with similar ecological niches and within the same geographic location. We assessed population genetics of congeneric and ecologically similar damselfishes within their overlapping distributions and across potential barriers to geneflow.</span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Taxon:</span></u></strong><span> <em>Dascyllus marginatus </em>(endemic) and <em>Dascyllus abudafur </em>(widespread)<em>.</em></span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Location:</span></u></strong><span> Coral reefs from the Red Sea, Djibouti, Yemen, Oman, and Madagascar. </span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Methods:</span></u></strong><span> We used RADseq derived SNPs to investigate key differences in population genetics between both species and discuss barriers shaping genetic differentiation (neutral vs. selective) and biogeography. </span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Results:</span></u></strong><strong><span> </span></strong><em><span>Dascyllus marginatus </span></em><span>inhabited the Red Sea, the coasts of Yemen (including Socotra), and the Gulf of Oman. <em>Dascyllus abudafur</em> species was present from the Red Sea to Madagascar but was absent from Yemen and Oman. Populations of <em>D. marginatus </em>had an order of magnitude higher genetic differentiation compared to <em>D. abudafur</em>, as well as several outlier loci (suggesting selective pressure), which were absent in <em>D. abudafur</em> despite equal sampling locations. In both species, specimens from the Red Sea and Djibouti formed one genetic cluster separated from all other locations. </span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Main conclusions:</span></u></strong><span> The stronger genetic structure at smaller geographic scale of the endemic species seems associated to faster adaptation to environmental differences; whereas the widespread species only experienced reduced geneflow and neutral differentiation at much larger geographic scales. Restrictive transitions (between the Gulf of Aqaba and the Red Sea or the Red Sea and the Gulf of Aden) did not affect the genetic architecture of either species, while the environmental shift within the Red Sea (at 22°N/20°N) affected the endemic but not the widespread species. Samples from continental Yemen revealed that a genetic break in the Gulf of Aden likely reflects historical colonization processes and not contemporary environmental regimes.</span></p>
Evaluating the use of non‐invasive hair sampling and ddRAD to characterize populations of endangered species: Application to a peripheral population of the European mink
<p>The application of next‐generation sequencing (NGS) to non‐invasive samples is one of the most promising methods in conservation genomics, but these types of samples present significant challenges for NGS. The European mink (<em>Mustela lutreola</em>) is critically endangered throughout its range. However, important aspects such as census size and inbreeding remain still unknown in many populations, so it is crucial to develop new methods to monitor this species. In this work, we placed hair tubes along riverbanks in a border area of the Iberian population, which allowed the genetic identification of 76 European mink hair samples. We then applied a reduced representation genomic sequencing (ddRAD) technique to a subset of these samples to test whether we could extract sufficient genomic information from them. We show that several problems with the DNA, including contamination, fragmentation, oxidation, and possibly sample mixing, affected the samples. Using various bioinformatic techniques to reduce these problems, we were able to unambiguously genotype 19 hair samples belonging to six individuals. This small number of individuals showed that the demographic status of the species in this peripheral population is worse than expected. The data obtained also allowed us to perform preliminary analyses of relatedness and inbreeding. Although further improvements in sampling and analysis are needed, the application of the ddRAD technique to non‐invasively obtained hairs represents a significant advance in the genomic study of endangered species.</p>
Illumina next generation ddRAD sequencing SNP data from: Contrasting genetic diversity and structure between endemic and widespread damselfishes are related to differing adaptive strategies
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Divergence time estimation using ddRAD data and an isolation-with-migration model applied to water vole populations of Arvicola
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<em>Scutellaria floridana</em> ddRAD-Seq vcf files
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ddRAD data for: Multiple introductions and overwintering shape the progressive invasion of Aedes albopictus beyond the Alps
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Evaluating the use of non‐invasive hair sampling and ddRAD to characterize populations of endangered species: Application to a peripheral population of the European mink
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Large‐scale genomic SNP dataset for central and southeast European Turkey oak (Quercus cerris L.) populations generated by ddRAD‐seq method
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Data from: Seascape genetics along environmental gradients in the Arabian Peninsula: insights from ddRAD sequencing of anemonefishes
Understanding the processes that shape patterns of genetic structure across space is a central aim of landscape genetics. However, it remains unclear how geographic features and environmental variables shape gene flow, particularly for marine species in large complex seascapes. Here, we evaluated the genomic composition of the two-band anemonefish Amphiprion bicinctus across its entire geographic range in the Red Sea and Gulf of Aden, as well as its close relative, Amphiprion omanensis endemic to the southern coast of Oman. Both the Red Sea and the Arabian Sea are complex and environmentally heterogeneous marine systems that provide an ideal scenario to address these questions. Our findings confirm the presence of two genetic clusters previously reported for A. bicinctus in the Red Sea. Genetic structure analyses suggest a complex seascape configuration, with evidence of both Isolation by Distance (IBD) and Isolation by Environment (IBE). In addition to IBD and IBE, genetic structure among sites was best explained when two barriers to gene flow were also accounted for. One of these coincides with a strong oligotrophic-eutrophic gradient at around 16-20˚N in the Red Sea. The other agrees with an historical bathymetric barrier at the straight of Bab al Mandab. Finally, these data support the presence of inter-specific hybrids at an intermediate suture zone at Socotra and indicate complex patterns of genomic admixture in the Gulf of Aden with evidence of introgression between species. Our findings highlight the power of recent genomic approaches to resolve subtle patterns of gene flow in marine seascapes.
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